from __future__ import division
from math import sqrt
from ase.atoms import Atoms
from ase.symbols import string2symbols
from ase.data import reference_states, atomic_numbers, chemical_symbols
from ase.utils import plural
[docs]def bulk(name, crystalstructure=None, a=None, c=None, covera=None, u=None,
orthorhombic=False, cubic=False):
"""Creating bulk systems.
Crystal structure and lattice constant(s) will be guessed if not
provided.
name: str
Chemical symbol or symbols as in 'MgO' or 'NaCl'.
crystalstructure: str
Must be one of sc, fcc, bcc, hcp, diamond, zincblende,
rocksalt, cesiumchloride, fluorite or wurtzite.
a: float
Lattice constant.
c: float
Lattice constant.
covera: float
c/a ratio used for hcp. Default is ideal ratio: sqrt(8/3).
u: float
Internal coordinate for Wurtzite structure.
orthorhombic: bool
Construct orthorhombic unit cell instead of primitive cell
which is the default.
cubic: bool
Construct cubic unit cell if possible.
"""
if covera is not None and c is not None:
raise ValueError("Don't specify both c and c/a!")
xref = None
ref = {}
if name in chemical_symbols:
Z = atomic_numbers[name]
ref = reference_states[Z]
if ref is not None:
xref = ref['symmetry']
structures = {'sc': 1, 'fcc': 1, 'bcc': 1, 'hcp': 1, 'diamond': 1,
'zincblende': 2, 'rocksalt':2, 'cesiumchloride':2,
'fluorite': 3, 'wurtzite': 2}
if crystalstructure is None:
crystalstructure = xref
if crystalstructure not in structures:
raise ValueError('No suitable reference data for bulk {}.'
' Reference data: {}'
.format(name, ref))
if crystalstructure not in structures:
raise ValueError('Unknown structure: {}.'
.format(crystalstructure))
# Check name:
n = len(string2symbols(name))
n0 = structures[crystalstructure]
if n != n0:
raise ValueError('Please specify {} for {} and not {}'
.format(plural(n0, 'atom'), crystalstructure, n))
if a is None:
if xref != crystalstructure:
raise ValueError('You need to specify the lattice constant.')
try:
a = ref['a']
except KeyError:
raise KeyError('No reference lattice parameter "a" for "{}"'
.format(name))
if crystalstructure in ['hcp', 'wurtzite']:
cubic = False
if c is not None:
covera = c / a
elif covera is None:
if xref == crystalstructure:
covera = ref['c/a']
else:
covera = sqrt(8 / 3)
if orthorhombic and crystalstructure != 'sc':
return _orthorhombic_bulk(name, crystalstructure, a, covera, u)
if cubic and crystalstructure in ['bcc', 'cesiumchloride']:
return _orthorhombic_bulk(name, crystalstructure, a, covera)
if cubic and crystalstructure != 'sc':
return _cubic_bulk(name, crystalstructure, a)
if crystalstructure == 'sc':
atoms = Atoms(name, cell=(a, a, a), pbc=True)
elif crystalstructure == 'fcc':
b = a / 2
atoms = Atoms(name, cell=[(0, b, b), (b, 0, b), (b, b, 0)], pbc=True)
elif crystalstructure == 'bcc':
b = a / 2
atoms = Atoms(name, cell=[(-b, b, b), (b, -b, b), (b, b, -b)],
pbc=True)
elif crystalstructure == 'hcp':
atoms = Atoms(2 * name,
scaled_positions=[(0, 0, 0),
(1 / 3, 2 / 3, 0.5)],
cell=[(a, 0, 0),
(-a / 2, a * sqrt(3) / 2, 0),
(0, 0, covera * a)],
pbc=True)
elif crystalstructure == 'diamond':
atoms = bulk(2 * name, 'zincblende', a)
elif crystalstructure == 'zincblende':
s1, s2 = string2symbols(name)
atoms = bulk(s1, 'fcc', a) + bulk(s2, 'fcc', a)
atoms.positions[1] += a / 4
elif crystalstructure == 'rocksalt':
s1, s2 = string2symbols(name)
atoms = bulk(s1, 'fcc', a) + bulk(s2, 'fcc', a)
atoms.positions[1, 0] += a / 2
elif crystalstructure == 'cesiumchloride':
s1, s2 = string2symbols(name)
atoms = bulk(s1, 'sc', a) + bulk(s2, 'sc', a)
atoms.positions[1, :] += a / 2
elif crystalstructure == 'fluorite':
s1, s2, s3 = string2symbols(name)
atoms = bulk(s1, 'fcc', a) + bulk(s2, 'fcc', a) + bulk(s3, 'fcc', a)
atoms.positions[1, :] += a / 4
atoms.positions[2, :] += a * 3 / 4
elif crystalstructure == 'wurtzite':
u = u or 0.25 + 1 / 3 / covera**2
atoms = Atoms(2 * name,
scaled_positions=[(0, 0, 0),
(1 / 3, 2 / 3, 0.5 - u),
(1 / 3, 2 / 3, 0.5),
(0, 0, 1 - u)],
cell=[(a, 0, 0),
(-a / 2, a * sqrt(3) / 2, 0),
(0, 0, a * covera)],
pbc=True)
else:
raise ValueError('Unknown crystal structure: ' + crystalstructure)
return atoms
def _orthorhombic_bulk(name, crystalstructure, a, covera=None, u=None):
if crystalstructure == 'fcc':
b = a / sqrt(2)
atoms = Atoms(2 * name, cell=(b, b, a), pbc=True,
scaled_positions=[(0, 0, 0), (0.5, 0.5, 0.5)])
elif crystalstructure == 'bcc':
atoms = Atoms(2 * name, cell=(a, a, a), pbc=True,
scaled_positions=[(0, 0, 0), (0.5, 0.5, 0.5)])
elif crystalstructure == 'hcp':
atoms = Atoms(4 * name,
cell=(a, a * sqrt(3), covera * a),
scaled_positions=[(0, 0, 0),
(0.5, 0.5, 0),
(0.5, 1 / 6, 0.5),
(0, 2 / 3, 0.5)],
pbc=True)
elif crystalstructure == 'diamond':
atoms = _orthorhombic_bulk(2 * name, 'zincblende', a)
elif crystalstructure == 'zincblende':
s1, s2 = string2symbols(name)
b = a / sqrt(2)
atoms = Atoms(2 * name, cell=(b, b, a), pbc=True,
scaled_positions=[(0, 0, 0), (0.5, 0, 0.25),
(0.5, 0.5, 0.5), (0, 0.5, 0.75)])
elif crystalstructure == 'rocksalt':
s1, s2 = string2symbols(name)
b = a / sqrt(2)
atoms = Atoms(2 * name, cell=(b, b, a), pbc=True,
scaled_positions=[(0, 0, 0), (0.5, 0.5, 0),
(0.5, 0.5, 0.5), (0, 0, 0.5)])
elif crystalstructure == 'cesiumchloride':
atoms = Atoms(name, cell=(a, a, a), pbc=True,
scaled_positions=[(0, 0, 0), (0.5, 0.5, 0.5)])
elif crystalstructure == 'wurtzite':
u = u or 0.25 + 1 / 3 / covera**2
atoms = Atoms(4 * name,
cell=(a, a * 3**0.5, covera * a),
scaled_positions=[(0, 0, 0),
(0, 1 / 3, 0.5 - u),
(0, 1 / 3, 0.5),
(0, 0, 1 - u),
(0.5, 0.5, 0),
(0.5, 5 / 6, 0.5 - u),
(0.5, 5 / 6, 0.5),
(0.5, 0.5, 1 - u)],
pbc=True)
else:
raise RuntimeError
return atoms
def _cubic_bulk(name, crystalstructure, a):
if crystalstructure == 'fcc':
atoms = Atoms(4 * name, cell=(a, a, a), pbc=True,
scaled_positions=[(0, 0, 0), (0, 0.5, 0.5),
(0.5, 0, 0.5), (0.5, 0.5, 0)])
elif crystalstructure == 'diamond':
atoms = _cubic_bulk(2 * name, 'zincblende', a)
elif crystalstructure == 'zincblende':
atoms = Atoms(4 * name, cell=(a, a, a), pbc=True,
scaled_positions=[(0, 0, 0), (0.25, 0.25, 0.25),
(0, 0.5, 0.5), (0.25, 0.75, 0.75),
(0.5, 0, 0.5), (0.75, 0.25, 0.75),
(0.5, 0.5, 0), (0.75, 0.75, 0.25)])
elif crystalstructure == 'rocksalt':
atoms = Atoms(4 * name, cell=(a, a, a), pbc=True,
scaled_positions=[(0, 0, 0), (0.5, 0, 0),
(0, 0.5, 0.5), (0.5, 0.5, 0.5),
(0.5, 0, 0.5), (0, 0, 0.5),
(0.5, 0.5, 0), (0, 0.5, 0)])
else:
raise RuntimeError
return atoms